in Four Easy Parts

Introduction

In this section the main properties of the 20 different
amino acids found in genetically encoded proteins will be
outlined. All amino acids have amino and carboxyl groups
attached to the alpha-carbon atom. When an amino acid is
incorporated into a polypeptide by the ribosome at say
position i in the sequence, it undergoes
a condensation reaction in which the carboxyl group of
the preceding amino acid (i-1) forms an amide (or peptide) bond
with the amino group residue i. In the next elongation cycle of
the ribosome, the carboxyl group of residue i becomes covalently
linked to the amino group of residue i+1 in the final sequence by
another peptide bond. Hence all amino acids in the protein are linked by
peptide bonds. In each condensation reaction an -OH group is
essentially lost from the participating carboxyl group and a
hydrogen is lost from the amino group, ie water is eliminated.
The amino group becomes a trigonal >N-H during this process.

The three-dimensional structure and function of a protein are
dependent on the sequence of amino acid side chains in the polypeptide.
Amino acid side chains can be divided into several different classes based
on their physico-chemical properties. The below diagram indicates the
colour scheme for the atoms in this section. Hydrogen atoms are not shown
for clarity and because they cannot be located in most protein X-ray structures.
In the diagrams the main chain carboxyl group of each amino acid is shown
only as a carbonyl (ie C=O) group as found in polypeptides.